Zinc in PDB 3kqi: Crystal Structure of PHF2 Phd Domain Complexed with H3K4ME3 Peptide

The structure of Crystal Structure of PHF2 Phd Domain Complexed with H3K4ME3 Peptide, PDB code: 3kqi was solved by H.Wen, J.Z.Li, T.Song, M.Lu, M.Lee, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	7.99 / 1.78
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	77.757, 77.758, 72.116, 90.00, 90.00, 120.00
R / Rfree (%)	19 / 21.8

The structure of Crystal Structure of PHF2 Phd Domain Complexed with H3K4ME3 Peptide also contains other interesting chemical elements:

Magnesium	(Mg)	2 atoms
Chlorine	(Cl)	1 atom

The binding sites of Zinc atom in the Crystal Structure of PHF2 Phd Domain Complexed with H3K4ME3 Peptide (pdb code 3kqi). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of PHF2 Phd Domain Complexed with H3K4ME3 Peptide, PDB code: 3kqi:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of PHF2 Phd Domain Complexed with H3K4ME3 Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of PHF2 Phd Domain Complexed with H3K4ME3 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn71 b:24.6 occ:1.00 SG A:CYS50 2.3 25.4 1.0 SG A:CYS26 2.3 25.7 1.0 SG A:CYS53 2.4 26.2 1.0 SG A:CYS23 2.4 22.4 1.0 CB A:CYS53 3.1 28.3 1.0 CB A:CYS23 3.1 24.0 1.0 CB A:CYS26 3.3 24.3 1.0 CB A:CYS50 3.5 25.5 1.0 N A:CYS26 3.7 24.6 1.0 N A:CYS50 4.0 24.8 1.0 CA A:CYS26 4.1 24.4 1.0 O A:HOH156 4.2 41.1 1.0 O A:HOH155 4.2 36.1 1.0 N A:CYS53 4.2 29.6 1.0 CA A:CYS53 4.3 29.2 1.0 CA A:CYS50 4.3 25.9 1.0 CE2 A:PHE30 4.3 22.7 1.0 CZ A:PHE30 4.4 24.0 1.0 CA A:CYS23 4.6 23.3 1.0 CB A:ALA25 4.6 24.9 1.0 C A:ALA25 4.8 25.0 1.0 O A:CYS50 4.9 26.2 1.0 C A:CYS50 4.9 26.8 1.0 C A:CYS26 5.0 24.2 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of PHF2 Phd Domain Complexed with H3K4ME3 Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of PHF2 Phd Domain Complexed with H3K4ME3 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn72 b:23.5 occ:1.00 ND1 A:HIS31 2.2 23.6 1.0 SG A:CYS34 2.3 24.0 1.0 SG A:CYS10 2.3 23.3 1.0 SG A:CYS8 2.3 23.2 1.0 CE1 A:HIS31 3.1 24.6 1.0 CG A:HIS31 3.2 23.4 1.0 CB A:CYS8 3.2 22.6 1.0 CB A:CYS34 3.2 25.6 1.0 CB A:CYS10 3.4 23.7 1.0 CB A:HIS31 3.5 23.1 1.0 O A:HOH122 3.5 27.0 1.0 N A:CYS10 3.9 23.8 1.0 N A:HIS31 4.1 23.0 1.0 NE2 A:HIS31 4.3 22.9 1.0 CA A:CYS10 4.3 23.3 1.0 CD2 A:HIS31 4.3 23.4 1.0 CA A:HIS31 4.4 23.2 1.0 O A:HOH135 4.5 35.7 1.0 NH2 A:ARG18 4.6 23.1 1.0 N A:VAL9 4.6 23.5 1.0 CA A:CYS8 4.6 22.6 1.0 CA A:CYS34 4.7 25.7 1.0 CG2 A:VAL9 4.7 25.2 1.0 C A:CYS8 4.9 23.4 1.0

H.Wen, J.Li, T.Song, M.Lu, P.Y.Kan, M.G.Lee, B.Sha, X.Shi. Recognition of Histone H3K4 Trimethylation By the Plant Homeodomain of PHF2 Modulates Histone Demethylation. J.Biol.Chem. V. 285 9322 2010.
ISSN: ISSN 0021-9258
PubMed: 20129925
DOI: 10.1074/JBC.C109.097667